From 7dce3919df85f5e7611f2030aaed50b790239930 Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Mon, 12 Aug 2024 23:38:06 +0200
Subject: [PATCH] Updated PhyloToL Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 ...oToL-Part-2:-MSAs,-trees,-and-contamination-loop.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 44de1f4..0a03149 100644
--- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -18,6 +18,16 @@ If you want to produce up to guidance files, you will change the default '--end
 If you want to start at a different point other than raw data, you will change the default '--start’ parameter to 'unaligned', 'aligned', or 'trees'. With these choices, this is the line you could run, with minimum requierements: 
 > python Scripts/phylotol.py --start raw --end trees --gf_list  listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder  > Output1.out
 
+**provides the table with list of options flags parameters here **
+
+Optional arguments can then be added to the command line, and will be described bellow.
+
+## Filtering on GC composition
+
+The filtering by GC content is done during pre-guidance and it selects only sequences that fall within a specified range (user defined ranges). 
+The renaming of each sequence is done using a utility script (GC_identifier.py) which renames the sequences with OGG, OG6, and OGA depending on if the sequence GC content falls below or above the user specified GC range. 
+The parameters for this when running pre-guidance is ‘--og_identifier’ and the options are 'OG','OG6','OGA','OGG' with the default being ‘OG’ and passing all the sequences to guidance without filtering.
+
 ## Overlap and similarity filters
 
 ## Guidance